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Aharon A, Benedek G, Barhoum B, Parnasa E, Magadle N, Perzon O, Mevorach D. HLA binding-groove motifs are associated with myocarditis induction after Pfizer-BioNTech BNT162b2 vaccination. Eur J Clin Invest 2024; 54:e14142. [PMID: 38071404 DOI: 10.1111/eci.14142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/16/2023] [Accepted: 11/25/2023] [Indexed: 03/13/2024]
Abstract
BACKGROUND AND AIMS We found a higher incidence of myocarditis in young males who had received at least two Pfizer-BioNTech BNT162b2 vaccinations. The human leukocyte antigens (HLA) are known to play an important role in infectious and autoinflammatory diseases. We hypothesized that certain HLA alleles might be associated with vaccination-induced myocarditis. METHODS HLA typing was performed using next-generation sequencing technology with the Illumina Iseq100 platform. HLA class I and II loci were genotyped in 29 patients with post-vaccination myocarditis and compared with HLA data from 300 healthy controls. RESULTS We demonstrate that the DRB1*14:01, DRB1*15:03 alleles and the motifs in HLA-A - Leu62 and Gln63, which are part of binding pocket B and HLA-DR Tyr47, His60, Arg70 and Glu74, which are part of binding pockets P4, P7 and P9, were significantly associated with disease susceptibility. CONCLUSIONS Our findings suggest that immunogenetic fingerprints in HLA peptide-binding grooves may affect the presentation of peptides derived from the Pfizer-BioNTech BNT162b2 vaccination to T cells and induce an inflammatory process that results in myocarditis.
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Affiliation(s)
- Aviran Aharon
- Hebrew University-Hadassah Faculty of Medicine, Jerusalem, Israel
| | - Gil Benedek
- Hebrew University-Hadassah Faculty of Medicine, Jerusalem, Israel
- Tissue Typing and Immunogenetics Unit, Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Barhoum Barhoum
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Elchanan Parnasa
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Nur Magadle
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ofer Perzon
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dror Mevorach
- Hebrew University-Hadassah Faculty of Medicine, Jerusalem, Israel
- Institute of Rheumatology-Immunology-Allergology and the Wohl Institute for Translational Medicine, Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Arrieta-Bolaños E, Hernández-Zaragoza DI, Barquera R. An HLA map of the world: A comparison of HLA frequencies in 200 worldwide populations reveals diverse patterns for class I and class II. Front Genet 2023; 14:866407. [PMID: 37035735 PMCID: PMC10076764 DOI: 10.3389/fgene.2023.866407] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
HLA frequencies show widespread variation across human populations. Demographic factors as well as selection are thought to have shaped HLA variation across continents. In this study, a worldwide comparison of HLA class I and class II diversity was carried out. Multidimensional scaling techniques were applied to 50 HLA-A and HLA-B (class I) as well as 13 HLA-DRB1 (class II) first-field frequencies in 200 populations from all continents. Our results confirm a strong effect of geography on the distribution of HLA class I allele groups, with principal coordinates analysis closely resembling geographical location of populations, especially those of Africa-Eurasia. Conversely, class II frequencies stratify populations along a continuum of differentiation less clearly correlated to actual geographic location. Double clustering analysis revealed finer intra-continental sub-clusters (e.g., Northern and Western Europe vs. South East Europe, North Africa and Southwest Asia; South and East Africa vs. West Africa), and HLA allele group patterns characteristic of these clusters. Ancient (Austronesian expansion) and more recent (Romani people in Europe) migrations, as well as extreme differentiation (Taiwan indigenous peoples, Native Americans), and interregional gene flow (Sámi, Egyptians) are also reflected by the results. Barrier analysis comparing DST and geographic location identified genetic discontinuities caused by natural barriers or human behavior explaining inter and intra-continental HLA borders for class I and class II. Overall, a progressive reduction in HLA diversity from African to Oceanian and Native American populations is noted. This analysis of HLA frequencies in a unique set of worldwide populations confirms previous findings on the remarkable similarity of class I frequencies to geography, but also shows a more complex development for class II, with implications for both human evolutionary studies and biomedical research.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Heidelberg, Germany
- *Correspondence: Esteban Arrieta-Bolaños,
| | | | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
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MHC Haplotyping of SARS-CoV-2 Patients: HLA Subtypes Are Not Associated with the Presence and Severity of COVID-19 in the Israeli Population. J Clin Immunol 2021; 41:1154-1161. [PMID: 34050837 PMCID: PMC8164405 DOI: 10.1007/s10875-021-01071-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
HLA haplotypes were found to be associated with increased risk for viral infections or disease severity in various diseases, including SARS. Several genetic variants are associated with COVID-19 severity. Studies have proposed associations, based on a very small sample and a large number of tested HLA alleles, but no clear association between HLA and COVID-19 incidence or severity has been reported. We conducted a large-scale HLA analysis of Israeli individuals who tested positive for SARS-CoV-2 infection by PCR. Overall, 72,912 individuals with known HLA haplotypes were included in the study, of whom 6413 (8.8%) were found to have SARS-CoV-2 by PCR. A total of 20,937 subjects were of Ashkenazi origin (at least 2/4 grandparents). One hundred eighty-one patients (2.8% of the infected) were hospitalized due to the disease. None of the 66 most common HLA loci (within the five HLA subgroups: A, B, C, DQB1, DRB1) was found to be associated with SARS-CoV-2 infection or hospitalization in the general Israeli population. Similarly, no association was detected in the Ashkenazi Jewish subset. Moreover, no association was found between heterozygosity in any of the HLA loci and either infection or hospitalization. We conclude that HLA haplotypes are not a major risk/protecting factor among the Israeli population for SARS-CoV-2 infection or severity. Our results suggest that if any HLA association exists with the disease it is very weak, and of limited effect on the pandemic.
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4
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High-resolution inference of genetic relationships among Jewish populations. Eur J Hum Genet 2020; 28:804-814. [PMID: 31919450 DOI: 10.1038/s41431-019-0542-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 09/25/2019] [Accepted: 10/13/2019] [Indexed: 11/08/2022] Open
Abstract
Recent studies have used genome-wide single-nucleotide polymorphisms (SNPs) to investigate relationships among various Jewish populations and their non-Jewish historical neighbors, often focusing on small subsets of populations from a limited geographic range or relatively small samples within populations. Here, building on the significant progress that has emerged from genomic SNP studies in the placement of Jewish populations in relation to non-Jewish populations, we focus on population structure among Jewish populations. In particular, we examine Jewish population-genetic structure in samples that span much of the historical range of Jewish populations in Europe, the Middle East, North Africa, and South Asia. Combining 429 newly genotyped samples from 29 Jewish and 3 non-Jewish populations with previously reported genotypes on Jewish and non-Jewish populations, we investigate variation in 2789 individuals from 114 populations at 486,592 genome-wide autosomal SNPs. Using multidimensional scaling analysis, unsupervised model-based clustering, and population trees, we find that, genetically, most Jewish samples fall into four major clusters that largely represent four culturally defined groupings, namely the Ashkenazi, Mizrahi, North African, and Sephardi subdivisions of the Jewish population. We detect high-resolution population structure, including separation of the Ashkenazi and Sephardi groups and distinctions among populations within the Mizrahi and North African groups. Our results refine knowledge of Jewish population-genetic structure and contribute to a growing understanding of the distinctive genetic ancestry evident in closely related but historically separate Jewish communities.
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5
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Ameen R, Al Shemmari SH, Marsh SGE. HLA Haplotype Frequencies and Genetic Profiles of the Kuwaiti Population. Med Princ Pract 2020; 29:39-45. [PMID: 30870850 PMCID: PMC7024892 DOI: 10.1159/000499593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The aim of this study was to assess the HLA haplotype frequencies and genetic profiles of the Kuwaiti population. MATERIALS AND METHODS Whole venous blood was obtained from 595 healthy, unrelated Kuwaiti volunteers. The study population was genotyped for HLA class I (HLA-A, HLA-B, and HLA-C) and class II (HLA-DRB1 and HLA-DQB1) loci using sequence-specific oligonucleotide (SSO) probe-based hybridization and high-resolution HLA genotyping. Haplotype frequencies were estimated using an implementation of the expectation maximization algorithm that resolves both phase and allelic ambiguity. The Kuwaiti population was compared with other populations from the US National Marrow Donor Program (NMDP), by running a principal component analysis (PCA) on the relevant haplotype frequencies. RESULTS The most common HLA class I alleles in Kuwait were HLA-A*02:01g, HLA-C*06:02g, and HLA-B*50:01g with frequencies of 16, 14, and 12%, respectively. The most common HLA class II alleles in Kuwait were HLA-DQB1*02:01g and HLA-DRB1*07:01 with frequencies of 29.7 and 16.5%, respectively. The most common Kuwaiti haplotype observed was HLA-A*02:01g∼HLA-C*06:02g∼HLA-B*50:01g∼HLA-DRB1*07:01∼HLA-DQB1*02:01g at a frequency of 2.3%. The PCA demonstrated close genetic proximity of the Kuwaiti population with Middle Eastern, Southeast Asian, and North African populations in the NMDP. CONCLUSION Identifying the haplotype diversity in the Kuwaiti population will contribute to the selection of an HLA-match for HSCT, disease associations, pharmacogenomics, and knowledge of pop-ulation HLA diversity.
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Affiliation(s)
- Reem Ameen
- Medical Laboratory Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait,
| | - Salem H Al Shemmari
- Medicine Department, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
| | - Steven G E Marsh
- Anthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, London, United Kingdom
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6
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Simanovsky AL, Madbouly A, Halagan M, Maiers M, Louzoun Y. Single haplotype admixture models using large scale HLA genotype frequencies to reproduce human admixture. Immunogenetics 2019; 71:589-604. [PMID: 31741008 DOI: 10.1007/s00251-019-01144-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/19/2019] [Indexed: 12/20/2022]
Abstract
The human leukocyte antigen (HLA) is the most polymorphic region in humans. Anthropologists use HLA to trace populations' migration and evolution. However, recent admixture between populations can mask the ancestral haplotype frequency distribution. We present a statistical method based on high-resolution HLA haplotype frequencies to resolve population admixture using a non-negative matrix factorization formalism and validated using haplotype frequencies from 56 world populations. The result is a minimal set of source components (SCs) decoding roughly 90% of the total variance in the studied admixtures. These SCs agree with the geographical distribution, phylogenies, and recent admixture events of the studied groups. With the growing population of multi-ethnic individuals, or individuals that do not report race/ethnic information, the HLA matching process for stem-cell and solid organ transplants is becoming more challenging. The presented algorithm provides a framework that facilitates the breakdown of highly admixed populations into SCs, which can be used to better match the rapidly growing population of multi-ethnic individuals worldwide.
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Affiliation(s)
| | - Abeer Madbouly
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Michael Halagan
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Martin Maiers
- Bioinformatics Research, Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Yoram Louzoun
- Department of Mathematics and Gonda brain research institute, Bar-Ilan University, 52900, Ramat-Gan, Israel.
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7
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Gladstein AL, Hammer MF. Substructured Population Growth in the Ashkenazi Jews Inferred with Approximate Bayesian Computation. Mol Biol Evol 2019; 36:1162-1171. [PMID: 30840069 DOI: 10.1093/molbev/msz047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The Ashkenazi Jews (AJ) are a population isolate sharing ancestry with both European and Middle Eastern populations that has likely resided in Central Europe since at least the tenth century. Between the 11th and 16th centuries, the AJ population expanded eastward leading to two culturally distinct communities in Western/Central and Eastern Europe. Our aim was to determine whether the western and eastern groups are genetically distinct, and if so, what demographic processes contributed to population differentiation. We used Approximate Bayesian Computation to choose among models of AJ history and to infer demographic parameter values, including divergence times, effective population sizes, and levels of gene flow. For the ABC analysis, we used allele frequency spectrum and identical by descent-based statistics to capture information on a wide timescale. We also mitigated the effects of ascertainment bias when performing ABC on SNP array data by jointly modeling and inferring SNP discovery. We found that the most likely model was population differentiation between Eastern and Western AJ ∼400 years ago. The differentiation between the Eastern and Western AJ could be attributed to more extreme population growth in the Eastern AJ (0.250 per generation) than the Western AJ (0.069 per generation).
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Affiliation(s)
- Ariella L Gladstein
- Department of Ecology, Evolution and Biology, University of Arizona, Tucson, AZ
| | - Michael F Hammer
- Arizona Research Laboratory Division of Biotechnology, University of Arizona, Tucson, AZ
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Osoegawa K, Mallempati KC, Gangavarapu S, Oki A, Gendzekhadze K, Marino SR, Brown NK, Bettinotti MP, Weimer ET, Montero-Martín G, Creary LE, Vayntrub TA, Chang CJ, Askar M, Mack SJ, Fernández-Viña MA. HLA alleles and haplotypes observed in 263 US families. Hum Immunol 2019; 80:644-660. [PMID: 31256909 DOI: 10.1016/j.humimm.2019.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 11/17/2022]
Abstract
The 17th International HLA and Immunogenetics Workshop (IHIW) conducted a project entitled "The Study of Haplotypes in Families by NGS HLA". We investigated the HLA haplotypes of 1017 subjects in 263 nuclear families sourced from five US clinical immunogenetics laboratories, primarily as part of the evaluation of related donor candidates for hematopoietic stem cell and solid organ transplantation. The parents in these families belonged to five broad groups - African (72 parents), Asian (115), European (210), Hispanic (118) and "Other" (11). High-resolution HLA genotypes were generated for each subject using next-generation sequencing (NGS) HLA typing systems. We identified the HLA haplotypes in each family using HaplObserve, software that builds haplotypes in families by reviewing HLA allele segregation from parents to children. We calculated haplotype frequencies within each broad group, by treating the parents in each family as unrelated individuals. We also calculated standard measures of global linkage disequilibrium (LD) and conditional asymmetric LD for each ethnic group, and used untruncated and two-field allele names to investigate LD patterns. Finally we demonstrated the utility of consensus DNA sequences in identifying novel variants, confirming them using HLA allele segregation at the DNA sequence level.
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Affiliation(s)
- Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Arisa Oki
- HLA Laboratory, City of Hope, Duarte, CA, USA
| | | | - Susana R Marino
- Transplant Immunology Laboratory, The University of Chicago Medicine, Chicago, IL, USA
| | - Nicholas K Brown
- Transplant Immunology Laboratory, The University of Chicago Medicine, Chicago, IL, USA
| | | | - Eric T Weimer
- Department of Pathology & Laboratory Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gonzalo Montero-Martín
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Lisa E Creary
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Tamara A Vayntrub
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | | | - Medhat Askar
- Baylor University Medical Center, Dallas, TX, USA
| | - Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Marcelo A Fernández-Viña
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
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9
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Zhong C, Gragert L, Maiers M, Hill BT, Garcia-Gomez J, Gendzekhadze K, Senitzer D, Song J, Weisenburger D, Goldstein L, Wang SS. The association between HLA and non-Hodgkin lymphoma subtypes, among a transplant-indicated population. Leuk Lymphoma 2019; 60:2899-2908. [PMID: 31215275 DOI: 10.1080/10428194.2019.1617858] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Several studies have implicated HLA in non-Hodgkin lymphoma (NHL) subtype etiology. However, NHL patients indicated for stem cell transplants are underrepresented in these reports. We therefore evaluated the association between HLA and NHL subtypes among a transplant-indicated population. One thousand three hundred and sixty-six NHL patients HLA-typed and indicated for transplant at the City of Hope National Medical Center (Duarte, CA) were compared to 10,271 prospective donors. Odds ratios and 95% confidence intervals were calculated for HLA haplotype and alleles, adjusted for sex and age. The HLA-A*0201∼C*0602∼B*1302∼DRB1*0701∼DQB1*0201 haplotype was significantly associated with follicular lymphoma (FL) risk among Caucasians. Several haplotypes were associated with diffuse large B-cell lymphoma (DLBCL) risk among Caucasians, including the previously implicated DLBCL risk loci, HLA-B*0801. The HLA-A*0101 allele was also observed to be associated with mantle cell lymphoma (MCL) risk. Our results support the association between previously reported susceptibility loci and FL and suggest potentially new DLBCL and MCL risk loci.
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Affiliation(s)
- Charlie Zhong
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA.,Bioinformatics Research, National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Brian T Hill
- Hematologic Oncology and Blood Disorders, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - David Senitzer
- Histocompatibility Laboratory, City of Hope, Duarte, CA, USA
| | - Joo Song
- Department of Pathology, City of Hope, Duarte, CA, USA
| | | | - Leanne Goldstein
- Division of Biostatistics, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Sophia S Wang
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
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Montero-Martín G, Mallempati KC, Gangavarapu S, Sánchez-Gordo F, Herrero-Mata MJ, Balas A, Vicario JL, Sánchez-García F, González-Escribano MF, Muro M, Moya-Quiles MR, González-Fernández R, Ocejo-Vinyals JG, Marín L, Creary LE, Osoegawa K, Vayntrub T, Caro-Oleas JL, Vilches C, Planelles D, Fernández-Viña MA. High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing. Hum Immunol 2019; 80:429-436. [PMID: 30763600 DOI: 10.1016/j.humimm.2019.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/07/2019] [Accepted: 02/09/2019] [Indexed: 12/25/2022]
Abstract
Next-generation sequencing (NGS) at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5 loci was performed on 282 healthy unrelated individuals from different major regions of Spain. High-resolution HLA genotypes defined by full sequencing of class I loci and extended coverage of class II loci were obtained to determine allele frequencies and also to estimate extended haplotype frequencies. HLA alleles were typed at the highest resolution level (4-field level, 4FL); with exception of a minor deviation in HLA-DPA1, no statistically significant deviations from expected Hardy Weinberg Equilibrium (HWE) proportions were observed for all other HLA loci. This study provides new 4FL-allele and -haplotype frequencies estimated for the first time in the Spanish population. Furthermore, our results describe extended haplotypes (including the less frequently typed HLA-DPA1 and HLA-DQA1 loci) and show distinctive haplotype associations found at 4FL-allele definition in this Spanish population study. The distinctive allelic and haplotypic diversity found at the 4FL reveals the high level of heterozygosity and specific haplotypic associations displayed that were not apparent at 2-field level (2FL). Overall, these results may contribute as a useful reference source for future population studies, for HLA-disease association studies as a healthy control group dataset and for improving donor recruitment strategies of bone marrow registries. HLA genotyping data of this Spanish population cohort was also included in the 17th International Histocompatibility and Immunogenetics Workshop (IHIW) as part of the study of HLA diversity in unrelated worldwide populations using NGS.
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Affiliation(s)
| | - Kalyan C Mallempati
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sridevi Gangavarapu
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - Antonio Balas
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - Jose L Vicario
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | | | | | - Manuel Muro
- Immunology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Maria R Moya-Quiles
- Immunology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | | | | | - Luis Marín
- Molecular Biology-Hematology, Hospital Clínico Universitario, Salamanca, Spain
| | - Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kazutoyo Osoegawa
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Tamara Vayntrub
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Jose L Caro-Oleas
- Histocompatibility and Immunogenetics, Banc de Sang i Teixits, Barcelona, Spain
| | - Carlos Vilches
- Immunogenetics and Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro, Madrid, Spain
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
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11
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Porriño-Bustamante ML, López-Nevot MÁ, Aneiros-Fernández J, Casado-Ruiz J, García-Linares S, Pedrinacci-Rodríguez S, García-Lora E, Martín-Casares MA, Fernández-Pugnaire MA, Arias-Santiago S. Study of Human Leukocyte Antigen (HLA) in 13 cases of familial frontal fibrosing alopecia: CYP21A2 gene p.V281L mutation from congenital adrenal hyperplasia linked to HLA class I haplotype HLA-A*33:01; B*14:02; C*08:02 as a genetic marker. Australas J Dermatol 2019; 60:e195-e200. [PMID: 30656636 DOI: 10.1111/ajd.12985] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/28/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND/OBJECTIVES The aetiology of frontal fibrosing alopecia is unknown, and its genetic aspect remains uncharacterised. The aim of this report is to elucidate if major histocompatibility complex is associated with familial frontal fibrosing alopecia. METHODS A case-control study was performed of 13 patients with frontal fibrosing alopecia belonging to six families. Their human leukocyte antigen profiles were compared to the data of 636 healthy controls without frontal fibrosing alopecia. Patients underwent high-resolution genomic typing for human leukocyte antigen class I and II loci by PCR-SSO for Luminex. In addition, CYP21A2 gene (major histocompatibility complex class III) mutations were detected by PCR-SSO on strips. RESULTS 61.5% of patients shared CYP21A2 gene p.V281L linked to the F16A human leukocyte antigen class I haplotype (HLA-A*33:01; B*14:02; C*08:02; Pc < 0.000001). The patients F16A-negative shared other human leukocyte antigen class I haplotypes: Y16A (3/13) and S26 (2/13). CONCLUSION CYP21A2 gene p.V281L mutation can be used as a genetic marker for susceptibility to familial frontal fibrosing alopecia. Both the linkage of the mutation to F16A and the fact that F16A-negative patients share other human leukocyte antigen class I haplotype, point to an antigen-driven mechanism in susceptible patients with these haplotypes.
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Affiliation(s)
| | - Miguel Ángel López-Nevot
- Laboratorio Clínico, Unidad de Histocompatibilidad, Hospital Universitario Virgen de las Nieves, Granada, Spain.,Departamento de Bioquímica, Biología Molecular III e Inmunología, Universidad de Granada, Granada, Spain
| | - José Aneiros-Fernández
- Servicio de Anatomía Patológica, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Jorge Casado-Ruiz
- Departamento de Bioquímica, Biología Molecular III e Inmunología, Universidad de Granada, Granada, Spain
| | - Susana García-Linares
- Unidad de Genética Clínica, Laboratorio Clínico, Hospital Universitario Virgen de las Nieves, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Susana Pedrinacci-Rodríguez
- Unidad de Genética Clínica, Laboratorio Clínico, Hospital Universitario Virgen de las Nieves, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Elena García-Lora
- Servicio de Dermatología, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | | | | | - Salvador Arias-Santiago
- Servicio de Dermatología, Hospital Universitario Virgen de las Nieves, Granada, Spain.,Facultad de Medicina, Universidad de Granada, Granada, Spain
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12
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Aboukaoud M, Israel S, Brautbar C, Eyal S. Genetic Basis of Delayed Hypersensitivity Reactions to Drugs in Jewish and Arab Populations. Pharm Res 2018; 35:211. [PMID: 30225831 DOI: 10.1007/s11095-018-2472-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/01/2018] [Indexed: 12/15/2022]
Abstract
Genetic variation can affect drug pharmacokinetics and pharmacodynamics and contribute to variability between individuals in response to medications. Specifically, differences in allele frequencies among individuals and ethnic groups have been associated with variation in their propensity to develop drug hypersensitivity reactions (HSRs). This article reviews the current knowledge on the genetic background of HSRs and its relevance to Jewish and Arab populations. The focus is on human leukocyte antigen (HLA) alleles and haplotypes as predictive markers of HSRs ("immunopharmacogenetics"), but other genes and alleles are described as well. Also discussed is the translation of the pharmacogenetic information to practice recommendations.
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Affiliation(s)
- Mohammed Aboukaoud
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Room 613, Ein Kerem, 91120, Jerusalem, Israel
| | - Shoshana Israel
- Tissue Typing Unit, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Chaim Brautbar
- Tissue Typing Unit, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Sara Eyal
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Room 613, Ein Kerem, 91120, Jerusalem, Israel.
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13
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Parks S, Avramopoulos D, Mulle J, McGrath J, Wang R, Goes FS, Conneely K, Ruczinski I, Yolken R, Pulver AE, Pearce BD. HLA typing using genome wide data reveals susceptibility types for infections in a psychiatric disease enriched sample. Brain Behav Immun 2018; 70:203-213. [PMID: 29574260 DOI: 10.1016/j.bbi.2018.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 02/27/2018] [Accepted: 03/03/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The infections Toxoplasma gondii (T. gondii), cytomegalovirus, and Herpes Simplex Virus Type 1 (HSV1) are common persistent infections that have been associated with schizophrenia and bipolar disorder. The major histocompatibility complex (MHC, termed HLA in humans) region has been implicated in these infections and these mental illnesses. The interplay of MHC genetics, mental illness, and infection has not been systematically examined in previous research. METHODS In a cohort of 1636 individuals, we used genome-wide association data to impute 7 HLA types (A, B, C, DRB1, DQA1, DQB1, DPB1), and combined this data with serology data for these infections. We used regression analysis to assess the association between HLA alleles, infections (individually and collectively), and mental disorder status (schizophrenia, bipolar disorder, controls). RESULTS After Bonferroni correction for multiple comparisons, HLA C∗07:01 was associated with increased HSV1 infection among mentally healthy controls (OR 3.4, p = 0.0007) but not in the schizophrenia or bipolar groups (P > 0.05). For the multiple infection outcome, HLA B∗ 38:01 and HLA C∗12:03 were protective in the healthy controls (OR ≈ 0.4) but did not have a statistically-significant effect in the schizophrenia or bipolar groups. T. gondii had several nominally-significant positive associations, including the haplotypes HLA DRB∗03:01 ∼ HLA DQA∗05:01 ∼ HLA DQB∗02:01 and HLA B∗08:01 ∼ HLA C∗07:01. CONCLUSIONS We identified HLA types that showed strong and significant associations with neurotropic infections. Since some of these associations depended on mental illness status, the engagement of HLA-related pathways may be altered in schizophrenia due to immunogenetic differences or exposure history.
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Affiliation(s)
- Samuel Parks
- Dept. of Epidemiology, Rollins School of Public Health, USA
| | - Dimitrios Avramopoulos
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer Mulle
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - John McGrath
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruihua Wang
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fernando S Goes
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Ingo Ruczinski
- Bloomberg School of Public Heath, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert Yolken
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ann E Pulver
- Bloomberg School of Public Heath, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brad D Pearce
- Dept. of Epidemiology, Rollins School of Public Health, USA.
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14
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Halagan M, Manor S, Shriki N, Yaniv I, Zisser B, Madbouly A, Maiers M, Stein J. East Meets West-Impact of Ethnicity on Donor Match Rates in the Ezer Mizion Bone Marrow Donor Registry. Biol Blood Marrow Transplant 2017; 23:1381-1386. [PMID: 28396163 DOI: 10.1016/j.bbmt.2017.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/05/2017] [Indexed: 11/24/2022]
Abstract
HLA haplotype frequencies in a volunteer bone marrow donor registry should reflect the frequencies of potential transplant recipients served by that registry, a challenge in a country with diverse subethnicities of immigrants from Eastern and Western cultures, such as Israel. We evaluated the likelihood of finding suitable donors for hypothetical patients drawn from defined subethnicities in the Ezer Mizion Bone Marrow Donor Registry (EM BMDR) from donors both within and outside the registry now and during the coming decade. On average, bioinformatics modeling predicts that, given current donor recruitment trends, 6/6 high-resolution HLA match rates for Israelis, which currently stand at 40% to 55% for most subethnicities, will rise by up to 1% per year over the next decade. Subethnicities with historically lower rates of interethnic admixture are less likely to find matches outside of their designated group but will benefit from expansion of the registry, whereas ethnically directed drives will enhance matching rates for currently underrepresented subethnicities. Donor searches for the same cohort using a large extramural registry was of only slight benefit for most of the 19 EM BMDR subethnicities evaluated, confirming that local donor registries that reflect the ethnic diversity of the community being served are best equipped to serve the needs of their respective communities. Contemporary trends of an increasingly multiethnic admixture in Israel may impact the effect of ethnic profiling in assessing future match rates for EM BMDR.
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Affiliation(s)
- Michael Halagan
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota.
| | - Sigal Manor
- Ezer Mizion Bone Marrow Donor Registry, Petah-Tikva, Israel
| | - Nira Shriki
- Ezer Mizion Bone Marrow Donor Registry, Petah-Tikva, Israel
| | - Isaac Yaniv
- Ezer Mizion Bone Marrow Donor Registry, Petah-Tikva, Israel; Bone Marrow Transplant Unit, Schneider Children's Medical Center of Israel, Petah-Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bracha Zisser
- Ezer Mizion Bone Marrow Donor Registry, Petah-Tikva, Israel
| | - Abeer Madbouly
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota
| | - Jerry Stein
- Bone Marrow Transplant Unit, Schneider Children's Medical Center of Israel, Petah-Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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15
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Maggio N, Firer M, Zaid H, Bederovsky Y, Aboukaoud M, Gandelman-Marton R, Noyman I, Ekstein D, Blatt I, Marom E, Schwartzberg E, Israel S, Ingber A, Brautbar C, Eyal S. Causative Drugs of Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis in Israel. J Clin Pharmacol 2017; 57:823-829. [PMID: 28181259 DOI: 10.1002/jcph.873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 12/16/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Nicola Maggio
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Maria Firer
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Huda Zaid
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yana Bederovsky
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mohammed Aboukaoud
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Revital Gandelman-Marton
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Neurology, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Iris Noyman
- Department of Pediatric Neurology, Soroka Medical Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Dana Ekstein
- Department of Neurology, Agnes Ginges Center for Human Neurogenetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ilan Blatt
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eli Marom
- Pharmaceutical Division, Israel Ministry of Health, Jerusalem, Israel
| | - Eyal Schwartzberg
- Pharmaceutical Division, Israel Ministry of Health, Jerusalem, Israel
| | - Shoshana Israel
- Tissue Typing Unit, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Arieh Ingber
- Department of Dermatology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Chaim Brautbar
- Tissue Typing Unit, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Sara Eyal
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
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16
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Dubois V, Detrait M, Sobh M, Morisset S, Labussière H, Giannoli C, Nicolini F, Moskovtchenko P, Mialou V, Ducastelle S, Rey S, Thomas X, Barraco F, Tedone N, Marry E, Garnier F, Bertrand Y, Michallet M. Using EasyMatch® to anticipate the identification of an HLA identical unrelated donor: A validated efficient time and cost saving method. Hum Immunol 2016; 77:1008-1015. [DOI: 10.1016/j.humimm.2016.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 02/16/2016] [Accepted: 02/18/2016] [Indexed: 02/01/2023]
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17
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Grubic Z, Maskalan M, Stingl Jankovic K, Zvecic S, Dumic Kubat K, Krnic N, Zunec R, Ille J, Kusec V, Dumic M. Association of HLA alleles and haplotypes with CYP21A2 gene p. V282L mutation in the Croatian population. HLA 2016; 88:239-244. [PMID: 27709802 DOI: 10.1111/tan.12907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/07/2016] [Accepted: 09/15/2016] [Indexed: 11/28/2022]
Abstract
The CYP21A2 mutations that are in linkage disequilibrium with particular HLA-A, -B, -DRB1 alleles/haplotypes, cause deficiency of the 21-hydroxylase enzyme (21-OHD) and account for the majority of congenital adrenal hyperplasia (CAH) cases. The aim of this study was to investigate those associations with the p.V282L mutation linked to the non-classical (NC) form of CAH among Croatians. The study included parents of patients with the NC form of CAH, positive for the p.V282L mutation (N = 55) and cadaveric donor samples (N = 231). All subjects were HLA-A, -B, and -DRB1 typed and tested for the presence of the p.V282L mutation. Among parents of patients, 92.73% of subjects were positive for the B*14:02 allele and almost half of them carried the HLA-A*33:01-B*14:02-DRB1*01:02 haplotype. Among cadaveric samples 77 out of 96 subjects positive for the B*14:02 allele had the p.V282L mutation. Among them, 37 were positive for the HLA-A*33:01-B*14:02-DRB1*01:02 haplotype, 23 had the HLA-A*33:01-B*14:02-DRB1*03:01 haplotype, 8 had the B*14:02-DRB1*01:02 combination and 5 were carrying the HLA-A*68:02-B*14:02-DRB1*13:03 haplotype. Only 4 of these subjects were positive for the B*14:02 allele. HLA-B*14:02 was the only single allele with association that reached statistically significant P value (RR = 12.00; P = 0.0024). Haplotypes B*14:02-DRB1*01:02 (P < 0.001) and HLA-A*68:02-B*14:02-DRB1*13:03 (P < 0.001) as well as HLA-A*33:01-B*14:02-DRB1*01:02 and HLA-A*33:01-B*14:02-DRB1*03:01 showed high relative risks (RR = 45.00, RR = 41.63 and RR = 36.96, respectively). Our data support the previously documented association of the HLA-A*33:01-B*14:02-DRB1*01:02 haplotype with the p.V282L mutation, but also point out a high frequency of the p.V282L mutation among Croatians with HLA-A*33:01-B*14:02-DRB1*03:01 and HLA-A*68:02-B*14:02-DRB1*13:03 haplotypes.
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Affiliation(s)
- Z Grubic
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, Clinical Hospital Centre Zagreb, Zagreb, Croatia.
| | - M Maskalan
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | - K Stingl Jankovic
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | - S Zvecic
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | - K Dumic Kubat
- Department of Pediatrics, Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | - N Krnic
- Department of Pediatrics, Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | - R Zunec
- Tissue Typing Centre, Department of Transfusion Medicine and Transplantation Biology, Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | - J Ille
- Department of Pediatrics, Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | - V Kusec
- Department of Laboratory Diagnosis, Clinical Hospital Centre Zagreb, Zagreb, Croatia
| | - M Dumic
- Department of Pediatrics, School of Medicine, Zagreb, Croatia
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18
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Manor S, Halagan M, Shriki N, Yaniv I, Zisser B, Maiers M, Madbouly A, Stein J. High-resolution HLA A∼B∼DRB1 haplotype frequencies from the Ezer Mizion Bone Marrow Donor Registry in Israel. Hum Immunol 2016; 77:1114-1119. [PMID: 27650516 DOI: 10.1016/j.humimm.2016.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 11/17/2022]
Abstract
We have investigated HLA population alleles and haplotype frequencies for the ethnicities that comprise the contemporary population of Israel, using a large data set from the Ezer Mizion Bone Barrow Donor Registry. We genotyped 275,699 individuals at the HLA-A, -B and -DRB1 loci using HLA genotyping methods. HLA A∼B∼DRB1 haplotype frequencies were estimated from 19 sub-ethnic Jewish populations and other non-Jewish minorities using the maximum likelihood model, which accommodates typing ambiguities. We present overall and sub-ethnicity specific HLA diversity results of the registry, which will help guide a data-driven strategy for future registry expansion.
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Affiliation(s)
- Sigal Manor
- Ezer Mizion Bone Marrow Donor Registry, Petach Tikva, Israel.
| | - Michael Halagan
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Nira Shriki
- Ezer Mizion Bone Marrow Donor Registry, Petach Tikva, Israel
| | - Isaac Yaniv
- Ezer Mizion Bone Marrow Donor Registry, Petach Tikva, Israel; Bone Marrow Transplant Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bracha Zisser
- Ezer Mizion Bone Marrow Donor Registry, Petach Tikva, Israel
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Abeer Madbouly
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA
| | - Jerry Stein
- Bone Marrow Transplant Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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19
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Israel S, Maggio N, Ekstein D, Zaid H, Firer M, Bederovsky Y, Noyman I, Gandelman-Marton R, Blatt I, Brautbar C, Marom E, Nahlieli Dil D, Berman E, Sabag D, Ingber A, Eyal S. Genetic risk factors for antiepileptic drug-induced hypersensitivity reactions in Israeli populations. Epilepsia 2016; 57:e205-e209. [DOI: 10.1111/epi.13498] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Shoshana Israel
- Tissue Typing Unit; Hadassah-Hebrew University Medical Center; Jerusalem Israel
| | - Nicola Maggio
- Department of Neurology; Sheba Medical Center; Tel Hashomer Israel
- Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Dana Ekstein
- Department of Neurology; Agnes Ginges Center for Human Neurogenetics; Hadassah-Hebrew University Medical Center; Jerusalem Israel
| | - Huda Zaid
- Institute for Drug Research; School of Pharmacy; The Hebrew University; Jerusalem Israel
| | - Maria Firer
- Institute for Drug Research; School of Pharmacy; The Hebrew University; Jerusalem Israel
| | - Yana Bederovsky
- Institute for Drug Research; School of Pharmacy; The Hebrew University; Jerusalem Israel
| | - Iris Noyman
- Department of Pediatric Neurology; Soroka Medical Center; Ben Gurion University of the Negev; Beer Sheva Israel
| | - Revital Gandelman-Marton
- Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv Israel
- Department of Neurology; Assaf Harofeh Medical Center; Zerifin Israel
| | - Ilan Blatt
- Department of Neurology; Sheba Medical Center; Tel Hashomer Israel
- Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv Israel
| | - Chaim Brautbar
- Tissue Typing Unit; Hadassah-Hebrew University Medical Center; Jerusalem Israel
| | - Eli Marom
- Department of Pharmacology; Israel Ministry of Health; Jerusalem Israel
| | | | - Erez Berman
- Department of Pharmacology; Israel Ministry of Health; Jerusalem Israel
| | - David Sabag
- Tissue Typing Unit; Hadassah-Hebrew University Medical Center; Jerusalem Israel
| | - Arieh Ingber
- Department of Dermatology; Hadassah-Hebrew University Medical Center; Jerusalem Israel
| | - Sara Eyal
- Institute for Drug Research; School of Pharmacy; The Hebrew University; Jerusalem Israel
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20
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Osoegawa K, Mack SJ, Udell J, Noonan DA, Ozanne S, Trachtenberg E, Prestegaard M. HLA Haplotype Validator for quality assessments of HLA typing. Hum Immunol 2015; 77:273-282. [PMID: 26546873 DOI: 10.1016/j.humimm.2015.10.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/29/2015] [Accepted: 10/29/2015] [Indexed: 11/15/2022]
Abstract
HLA alleles are observed in specific haplotypes, due to Linkage Disequilibrium (LD) between particular alleles. Haplotype frequencies for alleles in strong LD have been established for specific ethnic groups and racial categories. Application of high-resolution HLA typing using Next Generation Sequencing (NGS) is becoming a common practice in research and clinical laboratory settings. HLA typing errors using NGS occasionally occur due to allelic sequence imbalance or misalignment. Manual inspection of HLA genotypes is labor intensive and requires an in-depth knowledge of HLA alleles and haplotypes. We developed the "HLA Haplotype Validator (HLAHapV)" software, which inspects an HLA genotype for both the presence of common and well-documented alleles and observed haplotypes. The software also reports warnings when rare alleles, or alleles that do not belong to recognized haplotypes, are found. The software validates observable haplotypes in genotype data, providing increased confidence regarding the accuracy of the HLA typing, and thus reducing the effort involved in correcting potential HLA typing errors. The HLAHapV software is a powerful tool for quality control of HLA genotypes prior to the application of downstream analyses. We demonstrate the use of the HLAHapV software for identifying unusual haplotypes, which can lead to finding potential HLA typing errors.
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Affiliation(s)
- Kazutoyo Osoegawa
- Department of Pathology, Stanford University, Stanford, CA, USA; Children's Hospital Oakland Research Institute, Oakland, CA, USA.
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Julia Udell
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - David A Noonan
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
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21
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Khankhanian P, Matsushita T, Madireddy L, Lizée A, Din L, Moré JM, Gourraud PA, Hauser SL, Baranzini SE, Oksenberg JR. Genetic contribution to multiple sclerosis risk among Ashkenazi Jews. BMC MEDICAL GENETICS 2015. [PMID: 26212423 PMCID: PMC4557862 DOI: 10.1186/s12881-015-0201-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) is an autoimmune disease of the central nervous system, with a strong genetic component. Over 100 genetic loci have been implicated in susceptibility to MS in European populations, the most prominent being the 15:01 allele of the HLA-DRB1 gene. The prevalence of MS is high in European populations including those of Ashkenazi origin, and low in African and Asian populations including those of Jewish origin. METHODS Here we identified and extracted a total of 213 Ashkenazi MS cases and 546 ethnically matched healthy control individuals from two previous genome-wide case-control association analyses, and 72 trios (affected proband and two unaffected parents) from a previous genome-wide transmission disequilibrium association study, using genetic data to define Ashkenazi. We compared the pattern of genetic risk between Ashkenazi and non-Ashkenazi Europeans. We also sought to identify novel Ashkenazi-specific risk loci by performing association tests on the subset of Ashkenazi cases, controls, probands, and parents from each study. RESULTS The HLA-DRB1*15:01 allele and the non-HLA risk alleles were present at relatively low frequencies among Ashkenazi and explained a smaller fraction of the population-level risk when compared to non-Ashkenazi Europeans. Alternative HLA susceptibility alleles were identified in an Ashkenazi-only association study, including HLA-A*68:02 and one or both genes in the HLA-B*38:01-HLA-C*12:03 haplotype. The genome-wide screen in Ashkenazi did not reveal any loci associated with MS risk. CONCLUSION These results suggest that genetic susceptibility to MS in Ashkenazi Jews has not been as well established as that of non-Ashkenazi Europeans. This implies value in studying large well-characterized Ashkenazi populations to accelerate gene discovery in complex genetic diseases.
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Affiliation(s)
- Pouya Khankhanian
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.
| | - Takuya Matsushita
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA. .,Current address: Graduate School of Medical Sciences, Kyushu University School of Medicine, 3-1-1, Maidashi, Higashi-ku, Fukuoka City, 812-8582, Japan.
| | - Lohith Madireddy
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.
| | - Antoine Lizée
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.
| | - Lennox Din
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.
| | - Jayaji M Moré
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.
| | - Pierre-Antoine Gourraud
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.
| | - Stephen L Hauser
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.
| | - Sergio E Baranzini
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.
| | - Jorge R Oksenberg
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.
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22
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Comparison of high-resolution human leukocyte antigen haplotype frequencies in different ethnic groups: Consequences of sampling fluctuation and haplotype frequency distribution tail truncation. Hum Immunol 2015; 76:374-80. [PMID: 25637668 DOI: 10.1016/j.humimm.2015.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 01/16/2015] [Accepted: 01/21/2015] [Indexed: 11/23/2022]
Abstract
High-resolution haplotype frequency estimations and descriptive metrics are becoming increasingly popular for accurately describing human leukocyte antigen diversity. In this study, we compared sample sets of publically available haplotype frequencies from different populations to characterize the consequences of unequal sample size on haplotype frequency estimation. We found that for low samples sizes (a few thousand), haplotype frequencies were overestimated, affecting all descriptive metrics of the underlying distribution, such as most frequent haplotype, the number of haplotypes, and the mean/median frequency. This overestimation was a result of random sample fluctuation and truncation of the tail end of the frequency distribution that comprises the least frequent haplotypes. Finally, we simulated balanced datasets through resampling and contrasted the disparities of descriptive metrics among equal and unequal datasets. This simulation resulted in the global description of the most frequent human leukocyte antigen haplotypes worldwide.
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23
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Klitz W. Whitey crumbles. Trends Genet 2014; 30:516-8. [PMID: 25443044 DOI: 10.1016/j.tig.2014.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 10/07/2014] [Indexed: 12/01/2022]
Abstract
Despite scientific evidence to the contrary, cultural notions that incorrectly aggrandize genetic differences between ethnicities persist. New work on the genetic makeup of Europeans now shows even more definitively how false those notions are.
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Affiliation(s)
- William Klitz
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA.
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24
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Abstract
Chronic lymphocytic leukemia (CLL) displays remarkable ethnic predisposition for whites, with relative sparing of African-American and Asian populations. In addition, CLL displays among the highest familial predispositions of all hematologic malignancies, yet the genetic basis for these differences is not clearly defined. The highly polymorphic HLA genes of the major histocompatibility complex play a central role in immune surveillance and confer risk for autoimmune and infectious diseases and several different cancers, the role for which in the development of CLL has not been extensively investigated. The National Marrow Donor Program/Be The Match has collected HLA typing from CLL patients in need of allogeneic hematopoietic stem cell transplant and has recruited millions of volunteers to potentially donate hematopoietic stem cells. HLA genotypes for 3491 US white, 397 African-American, and 90 Hispanic CLL patients were compared with 50 000 controls per population from the donor registry. We identified several HLA alleles associated with CLL susceptibility in each population, reconfirming predisposing roles of HLA-A*02:01 and HLA-DRB4*01:01 in whites. Associations for haplotype DRB4*01:01∼DRB1*07:01∼DQB1*03:03 were replicated across all 3 populations. These findings provide a comprehensive assessment of the role of HLA in the development of severe CLL.
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Age-dependent HLA profiles of the Israeli population: impact on hematopoietic cell donor recruitment and availability. Immunogenetics 2014; 66:525-33. [DOI: 10.1007/s00251-014-0788-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 07/05/2014] [Indexed: 10/25/2022]
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Israeli M, Kristt D, Nardi Y, Klein T. Genetic considerations in human sex-mate selection: partners share human leukocyte antigen but not short-tandem-repeat identity markers. Am J Reprod Immunol 2014; 71:467-71. [PMID: 24589062 DOI: 10.1111/aji.12213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 01/13/2014] [Indexed: 11/26/2022] Open
Abstract
PROBLEM Previous studies support a role for MHC on mating preference, yet it remains unsettled as to whether mating occurs preferentially between individuals sharing human leukocyte antigen (HLA) determinants or not. Investigating sex-mate preferences in the contemporary Israeli population is of further curiosity being a population with distinct genetic characteristics, where multifaceted cultural considerations influence mate selection. METHOD OF STUDY Pairs of male-female sex partners were evaluated in three groups. Two groups represented unmarried (n = 1002) or married (n = 308) couples and a control group of fictitious male-female couples. HLA and short-tandem-repeat (STR) genetic identification markers were assessed for the frequency of shared antigens and alleles. RESULTS Human leukocyte antigen results showed that Class I and/ or Class II single antigen as well as double antigen sharing was more common in sex partners than in control group couples (P < 0.001). Married versus unmarried pairs were not distinguishable. In contrast, STR-DNA markers failed to differentiate between sex-mates and controls (P = 0.78). CONCLUSION Sex partnerships shared HLA determinants more frequently than randomly constituted male-female pairs. The observed phenomenon does not reflect a syngenetic background between sex-mates as STR markers were not selectively shared. Thus, sex-mate selection in man may contravene the evolutionary pressure for genetic diversity in regard to HLA.
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Affiliation(s)
- Moshe Israeli
- Tissue Typing Laboratory, Rabin Medical Center, Petach-Tikva, Israel
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Gragert L, Madbouly A, Freeman J, Maiers M. Six-locus high resolution HLA haplotype frequencies derived from mixed-resolution DNA typing for the entire US donor registry. Hum Immunol 2013; 74:1313-20. [DOI: 10.1016/j.humimm.2013.06.025] [Citation(s) in RCA: 275] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 06/06/2013] [Accepted: 06/14/2013] [Indexed: 11/24/2022]
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Israeli M, Yeshurun M, Stein J, Ram R, Shpilberg O, Levi CL, Klein T. Trends and challenges in searching for HLA-matched unrelated donors in Israel. Hum Immunol 2013; 74:942-5. [DOI: 10.1016/j.humimm.2013.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 04/09/2013] [Accepted: 04/12/2013] [Indexed: 10/26/2022]
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Klitz W, Gragert L, Trachtenberg E. Spectrum of HLA associations: the case of medically refractory pediatric acute lymphoblastic leukemia. Immunogenetics 2012; 64:409-19. [PMID: 22350167 PMCID: PMC3349849 DOI: 10.1007/s00251-012-0605-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 01/31/2012] [Indexed: 02/01/2023]
Abstract
Although studies of HLA and disease now date back some 50 years, a principled understanding of that relationship has been slow to emerge. Here, we examine the associations of three HLA loci with medically refractory pediatric acute lymphoblastic leukemia (pALL) patients in a case-control study involving 2,438 cases and 41,750 controls. An analysis of alleles from the class I loci, HLA-A and HLA-B, and the class II locus DRB1 illuminates a spectrum of extremely significant allelic associations conferring both predisposition and protection. Genotypes constructed from predisposing, protective, and neutral allelic categories point to an additive mode of disease causation. For all three loci, genotypes homozygous for predisposing alleles are at highest disease risk while the favorable effect of homozygous protective genotypes is less striking. Analysis of A-B and B-DRB1 haplotypes reveals locus-specific differences in disease effects, while that all three loci influence pALL; the influence of HLA-B is greater than that of HLA-A, and the predisposing effect of DRB1 exceeds that of HLA-B. We propose that the continuum in disease susceptibility suggests a system in which many alleles take part in disease predisposition based on differences in binding affinity to one or a few peptides of exogenous origin. This work provides evidence that an immune response mediated by alleles from several HLA loci plays a critical role in the pathogenesis of pALL, adding to the numerous studies pointing to a role for an infectious origin in pALL.
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Affiliation(s)
- William Klitz
- School of Public Health, University of California, Berkeley, CA, USA.
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Gourraud PA, Gilson L, Girard M, Peschanski M. The role of human leukocyte antigen matching in the development of multiethnic "haplobank" of induced pluripotent stem cell lines. Stem Cells 2012; 30:180-6. [PMID: 22045598 DOI: 10.1002/stem.772] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Among the tools of regenerative medicine, induced pluripotent stem cells (iPSCs) are interesting because the donor genotype can be selected. The construction of banks of iPSC cell lines selected from human leukocyte antigen (HLA) homozygous donors has been proposed to be an effective way to match a maximal number of patients receiving cell therapy from iPSC lines. However, what effort would be required to constitute such a bank for a worldwide application has remained unexplored. We developed a probabilistic model to compute the number of donors to screen for constituting banks of best-chosen iPSC lines with homozygous HLA haplotypes (haplobanks) in four ancestry backgrounds. We estimated what percentage of the patients would be provided with single HLA haplotype matched cell lines. Genetic diversity leads to different outcomes for the four sets in all terms. A bank comprising iPSC lines representing the 20 most frequent haplotypes in each population would request quite different number of donors to screen, between 26,000 for European Americans and 110,000 for African Americans. It would also match different fractions of the recipient population, namely, more than 50% of the European Americans and 22% of African Americans. Conversely, a bank comprising the 100 iPSC lines with the most frequent HLA in each population would leave out only 22% of the European Americans, but 37% of the Asians, 48% of the Hispanics, and 55% of the African Americans. The constitution of a haplobank of iPSC lines is achievable through a large-scale concerted worldwide collaboration.
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Affiliation(s)
- Pierre-Antoine Gourraud
- Department of Neurology, University of California San Francisco School of Medicine, San Francisco, California, USA.
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Fernandez Vina MA, Hollenbach JA, Lyke KE, Sztein MB, Maiers M, Klitz W, Cano P, Mack S, Single R, Brautbar C, Israel S, Raimondi E, Khoriaty E, Inati A, Andreani M, Testi M, Moraes ME, Thomson G, Stastny P, Cao K. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations. Philos Trans R Soc Lond B Biol Sci 2012; 367:820-9. [PMID: 22312049 DOI: 10.1098/rstb.2011.0320] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses. Therefore, allelic diversity in HLA should be analysed in conjunction with other genetic markers to accurately track the migrations of modern humans.
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Oksenberg JR, Klitz W. Immunogenetics in the Holy Land. TISSUE ANTIGENS 2010; 76:440-441. [PMID: 20860584 DOI: 10.1111/j.1399-0039.2010.01567.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- J R Oksenberg
- Department of Neurology, University of California, San Francisco, CA, USA.
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